###Guide to the BarkBase data site###

The files here complement and in some cases repeat those available through BarkBase (barkbase.org). They are organized as follows: 

RNA-seq/
	counts/  (N.B. In all cases, counts are offered for both genes and transcripts.)

	TMM_normalized/ - Matrices (.csv) of TMM-normalized counts (CPM) using the TMM method
	developed by Robinson and Oshlack  (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-3-r25).
	Values are provided for two different abundance thresholds:  CPM=0.16 (CPM_cutoff_0.16/) and CPM =1.0 (CPM_cutoff_1/).  

	raw_read_counts/ - Matrices (.csv) of raw read counts from each of the adult and embryonic samples.

	BarkBase_novel_transcripts.gtf Table - Tab seperated values (.tsv) of 2765 canine
		transcripts identified in BarkBase data, but not in earlier studies.

	GTF_files/ Zipped gtf files giving FPKM values, etc. for each adult and embryonic sample.

ATAC-seq_peak_files/ - ATAC-seq peak files for each tissue sample.

wgs_data/ - Varaint calls (versus CanFam3 reference) for each of the five adult dogs included in our study.

The paper presenting this work is available at https://www.mdpi.com/2073-4425/10/6/433

Initial date: June 6, 2019